Re: [galaxy-dev] Tool dependency installation fail, any documentation?
This page of the tool shed wiki has most of the details. The tool dependency tag definitions are evolving rapidly as more tools are being included in the Galaxy tool migration process. I'm trying to keep information updated, but at times the wiki page will lag due to resource deficiencies. http://wiki.galaxyproject.org/ToolShedToolFeatures Greg Von Kuster On Dec 12, 2012, at 7:01 PM, Franco Caramia wrote: Dave, Thanks for that, will pull the latest version and give it a go.. Is there any documentation on these tags and flags??? (tool dependencies installation) Cheers, Franco On 12/12/12 10:27 PM, Dave Bouvier d...@bx.psu.edu wrote: Franco, I see the issue, the target_file flag was introduced in 8268:87828175dfe7. If you update to the latest Galaxy dist release, that tool dependency xml should work just fine. --Dave B. On 2012-12-12 01:53, Franco Caramia wrote: Dave, It's : hg log | head changeset: 8153:5dcbbdfe1087 tag: tip user:Daniel Blankenberg d...@bx.psu.edu date:Tue Nov 06 12:57:23 2012 -0500 summary: Allow rerun to access hidden datasets. Thanks, Franco On 12/12/12 3:13 PM, Dave Bouvier d...@bx.psu.edu wrote: Franco, You're right, I see a both clean and all rules in the makefile. It looks almost like it's not finding the expected makefile, I'll have to look into that in the morning. As for the download_by_url action, it downloads and extracts the specified file, then changes to the extracted directory. Could you remind me which changeset revision you're trying to install this repository in? --Dave B. On 2012-12-11 23:10, Franco Caramia wrote: Hi Dave, It does not require it, but it should not fail either as the clean rule is in the makefile.. By removing it I get: make: *** No rule to make target `all'. Stop. Same problem as before but this time with the 'all' rule... I'm not sure what the action type=download_by_url tag does.. Do I need to 'cd' into the unzipped directory? Thanks, Franco On 12/12/12 1:03 PM, Dave Bouvier d...@bx.psu.edu wrote: Franco, BEDTools, unlike some other packages, does not require the 'make clean' shell command to compile. If you remove that line, the dependency should install without problems. --Dave B. On 2012-12-11 21:16, Franco Caramia wrote: Hi list, I got the following tool_dependencies.xml file failing: ?xml version=1.0? tool_dependency package name=bedtools version=2.17.0 install version=1.0 actions action type=download_by_url target_filename=bedtools-2.17.0.tar.gz http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz/action action type=shell_commandmake clean/action action type=shell_commandmake all/action action type=move_directory_files source_directorybin/source_directory destination_directory$INSTALL_DIR/bin/destination_directory /action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools /readme /package /tool_dependency The error given is: # make clean STDOUT # # make clean STDERR make: *** No rule to make target clean'. Stop. # I basically just copied the example code from the Galaxy wiki for R: ?xml version=1.0? tool_dependency set_environment version=1.0 environment_variable name=R_SCRIPT_PATH action=set_to$REPOSITORY_INSTALL_DIR/environment_variable /set_environment package name=R version=2.15.1 install version=1.0 actions action type=download_by_urlhttp://CRAN.R-project.org/src/base/R-2/R-2.15.1.ta r. gz /action action type=shell_command./configure --prefix=$INSTALL_DIR/action action type=shell_commandmake/action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. /readme /package /tool_dependency I have found no documentation to what the tag action type=download_by_url does... I have asumed it downloads, unzips and moves into the unzipped directory.. But apparently it doesn’t.. Any advice on this or at least a link to the pertinent documentation?? Thanks a lot in advance...
[galaxy-dev] Tool dependency installation fail, any documentation?
Hi list, I got the following tool_dependencies.xml file failing: ?xml version=1.0? tool_dependency package name=bedtools version=2.17.0 install version=1.0 actions action type=download_by_url target_filename=bedtools-2.17.0.tar. gz http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz/action action type=shell_commandmake clean/action action type=shell_commandmake all/action action type=move_directory_files source_directorybin/source_directory destination_directory$INSTALL_DIR/bin/destination_directory /action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DI R/bin/environment_variable /action /actions /install readme GCC version 4.1 or greater is recommended. 3.x versions will typically not c ompile BEDTools /readme /package /tool_dependency The error given is: # make clean STDOUT # # make clean STDERR make: *** No rule to make target clean'. Stop. # I basically just copied the example code from the Galaxy wiki for R: ?xml version=1.0? tool_dependency set_environment version=1.0 environment_variable name=R_SCRIPT_PATH action=set_to$REPOSITORY_INSTALL_DIR/environment_variable /set_environment package name=R version=2.15.1 install version=1.0 actions action type=download_by_urlhttp://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.g z/action action type=shell_command./configure --prefix=$INSTALL_DIR/action action type=shell_commandmake/action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. /readme /package /tool_dependency I have found no documentation to what the tag action type=download_by_url does... I have asumed it downloads, unzips and moves into the unzipped directory.. But apparently it doesn¹t.. Any advice on this or at least a link to the pertinent documentation?? Thanks a lot in advance... Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Tool dependency installation fail, any documentation?
Franco, BEDTools, unlike some other packages, does not require the 'make clean' shell command to compile. If you remove that line, the dependency should install without problems. --Dave B. On 2012-12-11 21:16, Franco Caramia wrote: Hi list, I got the following tool_dependencies.xml file failing: ?xml version=1.0? tool_dependency package name=bedtools version=2.17.0 install version=1.0 actions action type=download_by_url target_filename=bedtools-2.17.0.tar.gz http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz/action action type=shell_commandmake clean/action action type=shell_commandmake all/action action type=move_directory_files source_directorybin/source_directory destination_directory$INSTALL_DIR/bin/destination_directory /action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools /readme /package /tool_dependency The error given is: # make clean STDOUT # # make clean STDERR make: *** No rule to make target clean'. Stop. # I basically just copied the example code from the Galaxy wiki for R: ?xml version=1.0? tool_dependency set_environment version=1.0 environment_variable name=R_SCRIPT_PATH action=set_to$REPOSITORY_INSTALL_DIR/environment_variable /set_environment package name=R version=2.15.1 install version=1.0 actions action type=download_by_urlhttp://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz/action action type=shell_command./configure --prefix=$INSTALL_DIR/action action type=shell_commandmake/action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. /readme /package /tool_dependency I have found no documentation to what the tag action type=download_by_url does... I have asumed it downloads, unzips and moves into the unzipped directory.. But apparently it doesn’t.. Any advice on this or at least a link to the pertinent documentation?? Thanks a lot in advance... Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Tool dependency installation fail, any documentation?
Franco, You're right, I see a both clean and all rules in the makefile. It looks almost like it's not finding the expected makefile, I'll have to look into that in the morning. As for the download_by_url action, it downloads and extracts the specified file, then changes to the extracted directory. Could you remind me which changeset revision you're trying to install this repository in? --Dave B. On 2012-12-11 23:10, Franco Caramia wrote: Hi Dave, It does not require it, but it should not fail either as the clean rule is in the makefile.. By removing it I get: make: *** No rule to make target `all'. Stop. Same problem as before but this time with the 'all' rule... I'm not sure what the action type=download_by_url tag does.. Do I need to 'cd' into the unzipped directory? Thanks, Franco On 12/12/12 1:03 PM, Dave Bouvier d...@bx.psu.edu wrote: Franco, BEDTools, unlike some other packages, does not require the 'make clean' shell command to compile. If you remove that line, the dependency should install without problems. --Dave B. On 2012-12-11 21:16, Franco Caramia wrote: Hi list, I got the following tool_dependencies.xml file failing: ?xml version=1.0? tool_dependency package name=bedtools version=2.17.0 install version=1.0 actions action type=download_by_url target_filename=bedtools-2.17.0.tar.gz http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz/action action type=shell_commandmake clean/action action type=shell_commandmake all/action action type=move_directory_files source_directorybin/source_directory destination_directory$INSTALL_DIR/bin/destination_directory /action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools /readme /package /tool_dependency The error given is: # make clean STDOUT # # make clean STDERR make: *** No rule to make target clean'. Stop. # I basically just copied the example code from the Galaxy wiki for R: ?xml version=1.0? tool_dependency set_environment version=1.0 environment_variable name=R_SCRIPT_PATH action=set_to$REPOSITORY_INSTALL_DIR/environment_variable /set_environment package name=R version=2.15.1 install version=1.0 actions action type=download_by_urlhttp://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz /action action type=shell_command./configure --prefix=$INSTALL_DIR/action action type=shell_commandmake/action action type=set_environment environment_variable name=PATH action=prepend_to$INSTALL_DIR/bin/environment_variable /action /actions /install readme You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. /readme /package /tool_dependency I have found no documentation to what the tag action type=download_by_url does... I have asumed it downloads, unzips and moves into the unzipped directory.. But apparently it doesn¹t.. Any advice on this or at least a link to the pertinent documentation?? Thanks a lot in advance... Franco This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ This email (including any attachments or links) may contain confidential
